Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free standardized microenvironment. The hardness of the problem comes from the superposition between the driving forces of intra- and inter-molecule interactions and it is mirrored by the evidences of shift from folding to aggregation phenotypes by single-point mutations [10]. Here we apply several state-of-the-art classification methods coming from the field of structural pattern recognition, with the aim to compare different representations of the same proteins gathered from the Niwa et al. data base; such representations include sequences and labeled (contact) graphs enriched with chemico-physical attributes. By this comparison, we are able to identify also some interesting general properties of proteins. Notably, (i) we suggest a threshold around 250 residues discriminating "easily foldable" from "hardly foldable" molecules consistent with other independent experiments, and (ii) we highlight the relevance of contact graph spectra for folding behavior discrimination and characterization of the E. coli solubility data. The soundness of the experimental results presented in this paper is proved by the statistically relevant relationships discovered among the chemico-physical description of proteins and the developed cost matrix of substitution used in the various discrimination systems.Comment: 17 pages, 3 figures, 46 reference

A robust fuzzy possibilistic AHP approach for partner selection in international strategic alliance

The international strategic alliance is an inevitable solution for making competitive advantage and reducing the risk in today’s business environment. Partner selection is an important part in success of partnerships, and meanwhile it is a complicated decision because of various dimensions of the problem and inherent conflicts of stockholders. The purpose of this paper is to provide a practical approach to the problem of partner selection in international strategic alliances, which fulfills the gap between theories of inter-organizational relationships and quantitative models. Thus, a novel Robust Fuzzy Possibilistic AHP approach is proposed for combining the benefits of two complementary theories of inter-organizational relationships named, (1) Resource-based view, and (2) Transaction-cost theory and considering Fit theory as the perquisite of alliance success. The Robust Fuzzy Possibilistic AHP approach is a noveldevelopment of Interval-AHP technique employing robust formulation; aimed at handling the ambiguity of the problem and let the use of intervals as pairwise judgments. The proposed approach was compared with existing approaches, and the results show that it provides the best quality solutions in terms of minimum error degree. Moreover, the framework implemented in a case study and its applicability were discussed

An overview of decision table literature 1982-1995.

This report gives an overview of the literature on decision tables over the past 15 years. As much as possible, for each reference, an author supplied abstract, a number of keywords and a classification are provided. In some cases own comments are added. The purpose of these comments is to show where, how and why decision tables are used. The literature is classified according to application area, theoretical versus practical character, year of publication, country or origin (not necessarily country of publication) and the language of the document. After a description of the scope of the interview, classification results and the classification by topic are presented. The main body of the paper is the ordered list of publications with abstract, classification and comments.

Empirical models, rules, and optimization

This paper considers supply decisions by firms in a dynamic setting with adjustment costs and compares the behavior of an optimal control model to that of a rule-based system which relaxes the assumption that agents are explicit optimizers. In our approach, the economic agent uses believably simple rules in coping with complex situations. We estimate rules using an artificially generated sample obtained by running repeated simulations of a dynamic optimal control model of a firm's hiring/firing decisions. We show that (i) agents using heuristics can behave as if they were seeking rationally to maximize their dynamic returns; (ii) the approach requires fewer behavioral assumptions relative to dynamic optimization and the assumptions made are based on economically intuitive theoretical results linking rule adoption to uncertainty; (iii) the approach delineates the domain of applicability of maximization hypotheses and describes the behavior of agents in situations of economic disequilibrium. The approach adopted uses concepts from fuzzy control theory. An agent, instead of optimizing, follows Fuzzy Associative Memory (FAM) rules which, given input and output data, can be estimated and used to approximate any non-linear dynamic process. Empirical results indicate that the fuzzy rule-based system performs extremely well in approximating optimal dynamic behavior in situations with limited noise.Decision-making. ,econometric models ,TMD ,

Operational Decision Making under Uncertainty: Inferential, Sequential, and Adversarial Approaches

Modern security threats are characterized by a stochastic, dynamic, partially observable, and ambiguous operational environment. This dissertation addresses such complex security threats using operations research techniques for decision making under uncertainty in operations planning, analysis, and assessment. First, this research develops a new method for robust queue inference with partially observable, stochastic arrival and departure times, motivated by cybersecurity and terrorism applications. In the dynamic setting, this work develops a new variant of Markov decision processes and an algorithm for robust information collection in dynamic, partially observable and ambiguous environments, with an application to a cybersecurity detection problem. In the adversarial setting, this work presents a new application of counterfactual regret minimization and robust optimization to a multi-domain cyber and air defense problem in a partially observable environment

A Multi-Objective Optimization Approach for Multi-Head Beam-Type Placement Machines

This paper addresses a highly challenging scheduling problem in the field of printed circuit board (PCB) assembly systems using Surface Mounting Devices (SMD). After describing some challenging optimization sub-problems relating to the heads of multi-head surface mounting placement machines, we formulate an integrated multi-objective mathematical model considering of two main sub-problems simultaneously. The proposed model is a mixed integer nonlinear programming one which is very complex to be solved optimally. Therefore, it is first converted into a linearized model and then solved using an efficient multi-objective approach, i.e., the augmented epsilon constraint method. An illustrative example is also provided to show the usefulness and applicability of the proposed model and solution method.PCB assembly. Multi-head beam-type placement machine. Multi-objective mathematical programming. Augmented epsilon-constraint method

Name Strategy: Its Existence and Implications

It is argued that colour name strategy, object name strategy, and chunking strategy in memory are all aspects of the same general phenomena, called stereotyping, and this in turn is an example of a know-how representation. Such representations are argued to have their origin in a principle called the minimum duplication of resources. For most the subsequent discussions existence of colour name strategy suffices. It is pointed out that the Berlin†- Kay† universal partial ordering of colours and the frequency of traffic accidents classified by colour are surprisingly similar; a detailed analysis is not carried out as the specific colours recorded are not identical. Some consequences of the existence of a name strategy for the philosophy of language and mathematics are discussed: specifically it is argued that in accounts of truth and meaning it is necessary throughout to use real numbers as opposed to bi-valent quantities; and also that the concomitant label associated with sentences should not be of unconditional truth, but rather several real-valued quantities associated with visual communication. The implication of real-valued truth quantities is that the Continuum Hypothesis of pure mathematics is side-stepped, because real valued quantities occur ab initio. The existence of name strategy shows that thought/sememes and talk/phonemes can be separate, and this vindicates the assumption of thought occurring before talk used in psycho-linguistic speech production models.